Group Name |
Group Number |
Pure FR |
Alter method? |
SS prediction |
manual intervention |
homologues |
domain identification |
fragment-based approach |
use other servers |
lattice-based |
threading-like potentials |
relaxation/ optimization/ minimization |
other information |
SAM-T02-human |
001 |
N. Not exclusively FR, although a FR step was always part of the process. |
N |
Y. Four neural nets trained on STRIDE, DSSP, STR, ALPHA11 |
Y. Extensive manual intervention on the harder targets, assembling parts of the model by hand. Inspecting models, modifying cost function, re-optimizing, choosing models. |
Y. MSA for predicting secondary structure and building an HMM, which is then used for fold recognition and generating fragments. |
N. Generally started with whole chain, but sometimes broke this up into smaller pieces (not necessarily domains, as they sometimes overlapped) to repeat the fold recognition. |
Y. Three fragment sources: generic, specific and long-fragment libraries. |
Y. Used CAFASP output to confirm template selection; sometimes included Robetta models as possible conformations to modify in optimization process. |
N |
Y. Not a traditional pair-wise function, but a cost function based mostly on local environmental properties. Does not include hydrogen-bonding term, but does contain pairwise terms for cysteine residues. |
N |
- |
BAKER |
002 |
N |
Y. Predictions were ab initio modelled, or modelled in the context of a template, depending on PCons2 score. |
Y. PSIPred, Jufo, PHD |
Y. Domain parsing, model selection. |
Y. Secondary structure prediction, homologues predicted then clustered. |
Y. Ginzu (in-house) |
Y. Standard Rosetta library. |
Y. Pcons to screen targets. |
N |
Y. Knowledge-based potential, physically based potential. |
Y. Monte Carlo minimization; side-chains repacked using MC search through Dunbrack's rotamer library. |
- |
Skolnick-Kolinski |
010 |
N. Uses FR to generate predicted contacts, but these need not come from proteins with the same global fold. |
N |
Y. PSIPred |
N |
Y. Multiple sequence alignments used to build profiles for threading-based contact prediction. Pair potentials averaged over homologues. |
N. Domains were only identified if more than one template was found during the threading stage. |
N |
N |
Y |
Y. Pair, burial, secondary structure prediction. |
Y. Assembly using replica exchange Monte Carlo. |
- |
ORNL-PROSPECT |
012 |
Y |
N |
Y. PROSPECT-SSP (in-house program) |
Y. Adjustments to minimize the number of long gaps and achieve better structural quality scores, assessed by WhatIf. |
Y. Profile-profile alignment. |
Y. Prodom |
N |
N |
N |
Y. Environment-specific (singleton) and pair contact potentials. |
N |
This is the manual version of group 195 (ORNL-PROSPECT server). |
S:BAKER-ROBETTA |
029 |
N |
Y. Predictions were ab initio modelled, or modelled in the context of a template, depending on PCons2 score. |
Y. PSIPred, SAM-T99, JUFO. |
N |
Y. Structures generated for family members then clustered; largest composite clusters submitted as predictions. |
Y. Ginzu (in-house) |
Y. Standard Rosetta library. |
Y. Pcons to find ab initio targets. |
N |
Y. Environment and residue pair potentials. |
N. Robetta uses only a low resolution centroid based representation of sidechains and a straight Monte Carlo search strategy. |
- |
S:Pmodel |
040 |
Y |
N |
Y. PSIPred |
N |
N |
N |
N |
Y. Consensus of mGenThreader, FFAS, Inbgu, 3D-PSSM, PDB-BLAST, SAM-T99, FUGUE. |
N |
N |
N |
- |
S:Pmodel3 |
045 |
Y |
N |
Y. PSIPred |
N |
N |
N |
N |
Y. Consensus of INBGU-SHGU, FUGUE-2.1, ORFeus. |
N |
N |
N |
- |
SAMUDRALA-NEWFOLD |
051 |
N |
N |
Y. PSIPred |
N. Method is completely automated. |
N |
Y. Domains were defined based on the number of secondary structure elements (in-house algorithm). |
Y. About 30% of moves came from a 3-residue fragments of identical sequence. |
N |
N |
Y. All-atom residue-specific conditional probability scoring function (similar to potential of mean force used by Sippl). |
Y. ENCAD was used to eliminate any atom-atom overlaps and fix minor steric problems. |
Same method as used by group 140. |
Jones-NewFold |
068 |
N |
N |
Y. PSIPred |
N |
Y. Energies are averaged over a set of aligned homologous sequences (created using PSI-BLAST). |
N. Apart from removing domains with obvious sequence similarities. |
Y. Library of super-secondary motifs and 3-5 residue fragments extracted from 200 high-resolution structures. |
N |
N |
Y. THREADER3 potentials: beta-carbon distance-based potentials of mean force. |
N |
- |
Friesner |
112 |
N. A combination of fold recognition and simulation methods were used, depending on the target. |
Y. Different methods were used for alpha-helical and mixed alpha-beta proteins. |
Y. All secondary structure prediction methods used. |
Y. Visual inspection of models. |
Y. Multiple sequence information used to contruct profiles in threading. |
Y. In some cases identified likely domains from secondary structure prediction. |
N |
N |
N |
Y. Statistical size-dependent potential. |
Y. Simulations involved Monte Carlo moves followed by minimization. |
- |
S:I-Sites/Bystroff |
132 |
N |
Y. If the target has a PSI-BLAST hit, the alignment is used to assign coordinates. |
Y. HMMSTR. |
N |
Y. PSI-BLAST. |
N. Although sequences were split into overlapping domain-sized segments. |
Y. I-sites library. |
N |
N |
N |
Y. Rosetta minimizes the energy during the simulation. |
|
S:PROTINFO-AB |
140 |
N |
N |
Y. PSIPred |
N |
N |
Y. Domains were defined based on the number of secondary structure elements (in-house algorithm). |
Y. About 30% of moves came from a 3-residue fragments of identical sequence. |
N |
N |
Y. All-atom residue-specific conditional probability scoring function (similar to potential of mean force used by Sippl). |
Y. ENCAD was used to eliminate any atom-atom overlaps and fix minor steric problems. |
Same method as used by group 051. |
FAMS |
168 |
Y |
N |
Y. PSIPred |
N |
N |
N |
N |
N |
N |
N |
Y. Simulated annealing process using homology modelling software, FAMS. |
- |
ORNL-PROSPECT |
195 |
Y |
N |
Y. PROSPECT-SSP (in-house program) |
N |
Y. Profile-profile alignment. |
N |
N |
N |
N |
Y. Environment-specific (singleton) and pair contact potentials. |
N |
This is the automatic server. Group 012 combines the server with manual intervention. |
Pushchino |
203 |
N |
N |
Y. Mainly PSIPred, but also Jpred, ALB (in-house). |
Y. Visual inspection of alignments and/or models. |
Y. Sequence and secondary structure profile used in threading. |
Y. Identified domains using PSI-BLAST, HMMer and an in-house method. |
N. Sometimes visual inspection led to good predictions of fragments being merged into a joint model. |
N |
N |
Y. SCF_THREADER uses empirical potentials of short-range interactions |
N |
- |
3D-PSSM |
229 |
Y |
N |
Y. PSIPred |
N. Fully automated server. |
Y. Template sequences aligned to PSI-BLAST target sequence profile. |
N |
N |
N |
N |
Y. Jones' THREADER solvation potential. |
N |
- |
Head-Gordon |
271 |
N |
N |
Y. PSIPred |
Y. Visual inspection during global optimization. |
N |
N |
N |
Y. Used CAFASP summaries to screen out easy FR and CM targets. |
N |
N. Physical all atom force field (AMBER) and hydrophobic solvation term derived in-house. |
Y. Method focusses exclusively on local/global optimization. |
- |
Wolynes-Schulten |
294 |
N |
N |
Y. Jpred and also a consensus based on PSIpred, PHD, Jpred, SSPro, and Prof. |
Y. Visual inspection of top-scoring structures. |
Y |
Y. Variety of methods used: a search for exon/intron boundaries, examination of multiple sequence profiles, and results from the PRODOM and CAFASP servers. |
N |
Y. CAFASP used to screen targets. |
N |
Y. Associative memory terms combined with optimized contact potential and conventional threading potential (which contains pair, hydrogen bond, and profile potentials with a position dependent gap penalty). |
Y. Energy function minimized using molecular dynamics with simulated annealing. |
- |
Scheraga-Harold |
314 |
N |
N |
Y. Jnet, Jpred |
Y. In most cases, final structures were selected by visual inspection. |
N |
Y. In some cases, domain definitions were based on CAFASP results. |
N |
Y. CAFASP results were used to detect domains. |
N |
N. Used a physics-based energy function (UNRES) with long-range and short-range energy components (including correlation terms). |
Y. Conformational space annealing; energy minimization. |
- |
Shortle |
349 |
N |
N |
Y. PSIPred, in-house method. |
Y. Extensive visual creation/inspection of models. |
Y. Used homologoues in secondary structure prediction and threading to find fragments. |
N. Although sequences were often subdivided, with dividing lines between segments at high turn propensity and low hydrophobicity. |
Y. Dunbrack's culled PDB set. |
Y. PSI-BLAST was used to remove comparative modelling targets. Looked at output of some CAFASP secondary structure servers. |
N |
Y. Lawrence & Bryant's empirical pair potentials and in-house phi/psi/rotamer propensities and beta-carbon burial propensities |
N |
- |
Brooks |
373 |
N. Templates were used in cases where alignments were sufficiently good to allow the construction of reasonable (partial) 3D skeletons in agreement with secondary structure predictions. |
Y. Ab initio was used whenever sufficient template information was not available. |
Y. Consensus of PSIPred, PHD, SAM-T99, SSpro, as a bias for conformational searching. |
Y. Visual inspection to select initial templates, manual docking of domains in some cases. |
N |
Y. In some cases, domains sampled separately then combined to a single structure. Domain boundaries identified based on alignment with different templates at different parts of the sequence. |
N |
Y. CAFASP servers were used to find templates. |
Y. Ranking and refinement of structures was done using all-atom continuous-space models. |
N |
Y. All-atom force-field minimization and molecular dynamics for ranking and refinement. |
- |
Doniach |
401 |
N |
N |
Y. PSIPred |
Y. Picking and ranking submissions. |
N |
Y. PSI-BLAST |
N |
Y. GenTHREADER used to screen targets. |
N |
N |
N |
- |
TOME |
450 |
Y |
N |
Y. Predictions from JPred2 and those included in 3D-PSSM, mGenTHREADER or SAM-T99. |
Y. Choice of template. |
Y. Multiple sequence alignments re-threaded onto template to assess structural alignments. |
Y. Domains sometimes assigned after initial threading runs identified regions corresponding to templates shorted than the target. |
N |
Y. Metaserver uses BLAST, 3D-PSSM, mGenTHREADER, FUGUE, SAM-T99 and JPred2. |
N |
Y. Pair potential derived from PKB (sidechain/sidechain interactions only). |
N. Only when the model was built using MODELLER. |
Main difference between this group and group 464 is choice of template. |
ATOME |
464 |
Y |
N |
Y. Predictions from JPred2 and those included in 3D-PSSM, mGenTHREADER or SAM-T99. |
N |
Y. Multiple sequence alignments re-threaded onto template to assess structural alignments. |
N |
N |
Y. Metaserver uses BLAST, 3D-PSSM, mGenTHREADER, FUGUE, SAM-T99 and JPred2. |
N |
Y. Pair potential derived from PKB (sidechain/sidechain interactions only). |
N. Only when the model was built using MODELLER. |
Main difference between this group and group 450 is choice of template. |
GeneSilico |
517 |
Y |
N |
Y. Consensus based on PSIPred, PHD, PROF, APSSP, Jpred, SSPRO. |
Y. Manual intervention at all stages, including generation of hybrid templates, alignment refinement, and partial rebuilding of backbone and sidechains. |
Y |
Y. Fold recognition servers and secondary structure prediction; sequences split manually. |
Y. Fragments from original fold recognition models, which were positively evaluated using Verify3D. |
N. Used GeneSilico server. |
N |
N |
N |
Modified fold recognition approach, selecting best supersecondary structures, optimizing and merging manually. |